combine_predict_grid: Combine prediction grid list into a result object. Exposure...
In campbio/BAGEL: Novel Mutational Signature Analysis

Description Usage Arguments Value Examples

Combine prediction grid list into a result object. Exposure values are zero for samples in an annotation where that signature was not predicted

1	combine_predict_grid(grid_list, bagel, signature_res)

`grid_list`	A list of result objects from the prediction grid to combine into a single result
`bagel`	Input samples to predit signature weights
`signature_res`	Signatures to automatically subset from for prediction

A result object combining all samples and signatures from a prediction grid. Samples have zero exposure value for signatures not found in that annotation type.

bay <- readRDS(system.file("testdata", "bagel_annot.rds", package = "BAGEL"))
grid <- auto_predict_grid(bay, "SBS96", BAGEL::cosmic_v2_sigs, "lda",
"Tumor_Subtypes", combine_res = FALSE)
combined <- combine_predict_grid(grid, bay, BAGEL::cosmic_v2_sigs)
plot_exposures_by_annotation(combined, "Tumor_Subtypes")